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At least 1,639 records · Page 91

Is the Supporting Information the Venue for Reproducibility and Transparency?

Making research data, software, and data processing tools readily available to the public could significantly enhance the impact of scientific publications. Openness and transparency could address reproducibility concerns and accelerate scientific progress.(1, 2) While archives and repositories would be preferable for securing data in the long term, the Supporting Information (SI) already allocates significant space to provide auxiliary files, links, and essential information needed to make scientific findings immediately reproducible as well as data processing protocols and numerical procedures executable. Furthermore, the SI document could ensure that data that might not fit in the tight confines of a journal article lives online even when laboratories move on to other projects, close, and lose track of their data. The change for openness and transparency might be difficult to embrace, depending on the specific nature of the project. Nevertheless, the trend to make raw research data and open-source software packages available to the public has been building steady momentum. Openness in research data and software sharing is already making transformative contributions to the communication of research findings, critical for ensuring reproducibility as well as training of the next generation of scientists.

Rudshteyn, Benjamin↗

Using Atom Dynamics to Map the Defect Structure Around an Impurity in Nano-Hematite

The geochemical cycling of actinides such as U is strongly controlled by Fe (oxyhydr)oxides. Indeed, the strong affinity of these minerals for U has factored into the design of geologic repositories for the long-term storage of nuclear waste. Many decades of work have focused on detailing the local coordination environment U associated with hematite (a-Fe2O3), a common and stable Fe(III) oxide, in order to better predict the fate and transport of U in the sub-surface. Here, for the first time, molecular dynamic simulations and atomically resolved electron microscopy of uranium atom mobility under the beam were used to map the topology of defect clusters surrounding structurally incorporated U in hematite. The ability to observe vacancies by means of metal atom hopping can be used to directly probe defects in other materials, with promising applications in geochemistry and materials science.

Ilton, Eugene S.↗

Compensatory islet response to insulin resistance revealed by quantitative proteomics

Compensatory islet response is a distinct feature of the pre-diabetic insulin resistant state in humans and rodents. To identify alterations in the islet proteome that characterize the adaptive response, we analyzed islets from five-month-old male control, high-fat diet fed (HFD) or obese ob/ob mice by LC-MS(/MS) and quantified ~1,100 islet proteins (at least two peptides) with a false discovery rate <1%. Significant alterations in abundance were observed for ~350 proteins between groups. A majority of alterations were common to both models, and the changes of a subset of ~40 proteins and 12 proteins were verified by targeted quantification using selected reaction monitoring and Western blots, respectively. The insulin resistant islets in both groups exhibited reduced expression of proteins controlling energy metabolism, oxidative phosphorylation, hormone processing, and secretory pathways. Conversely, an increased expression of molecules involved in protein synthesis and folding suggested effects in endoplasmic reticulum stress response, cell survival, and proliferation in both insulin resistant models. In conclusion, we report a unique comparison of the islet proteome that is focused on the compensatory response in two insulin resistant rodent models that are not overtly diabetic. In conclusion, these data provide a valuable resource of candidate proteins to the scientific community to undertake further studies aimed at enhancing β-cell mass in patients with diabetes. The data are available via the MassIVE repository, with accession MSV000079093.

59 BASIC BIOLOGICAL SCIENCES↗

Transformation of Ferrihydrite to Goethite and the Fate of Plutonium

Understanding the interactions between plutonium and iron (oxy)hydroxide minerals is necessary to gain a predictive understanding of plutonium environmental mobility and to evaluate long-term performance of nuclear waste repositories. We investigated the fate of plutonium during the formation of ferrihydrite and its subsequent transformation into goethite. Ferrihydrite was synthesized with varying quantities of Pu(IV) following either a sorption or coprecipitation process; the ferrihydrite was then aged hydrothermally to yield goethite. Additionally, the synthesized materials were characterized via extended X-ray absorption fine structure spectroscopy, transmission electron microscopy, and acid leaching to elucidate the nature of plutonium association with ferrihydrite and goethite. In samples prepared following the sorption method, plutonium was identified in two different forms: a PuO 2 precipitate and a surface-sorbed plutonium complex. For the samples prepared via coprecipitation, no PuO 2 formation occurs in the ferrihydrite precursor and in the goethite experiments where plutonium concentration is ≤1000 ppm (mg kg –1 ). In these coprecipitation products, plutonium is strongly bound to the minerals either via formation of an inner sphere complex, or via an incorporation process. In the coprecipitation experiments, PuO 2 formation only occurs at the highest plutonium concentration (3000 ppm), suggesting that during ferrihydrite transformation into goethite, part of the plutonium can be remobilized to form PuO 2 nanoparticles. Collectively, our results demonstrate that the nature of plutonium associated with the precursor ferrihydrite (adsorbed vs coprecipitated) will have a direct impact on the association of plutonium with its alteration product (goethite). Furthermore, the data illustrate that some properties of plutonium association with the precursor ferrihydrite are retained through the transformation into goethite. These findings show that plutonium strongly associates with iron (oxy)hydroxides formed through coprecipitation processes and in these materials, plutonium can be strongly retained by the iron minerals.

54 ENVIRONMENTAL SCIENCES↗

High-Temperature Thermodynamics of Cerium Silicates, A-Ce 2 Si 2 O 7 , and Ce 4.67 (SiO 4 ) 3 O

Lanthanide disilicates and oxyapatites have potential roles in high temperature applications as thermal (TBC) and environmental barrier coatings (EBC), or possible alteration phases in geological nuclear waste repositories. However, those Ce 3+ -bearing silicates have only been limitedly studied. In this work, we performed detailed structural and thermodynamic investigations on A-Ce 2 Si 2 O 7 (tetragonal, P4 1 ) and Ce 4.67 (SiO 4 ) 3 O (hexagonal, P6 3 /m). The high temperature structural behaviors and coefficients of thermal expansion were determined by in situ high temperature synchrotron X-ray diffraction (HT-XRD) implemented with Rietveld analysis and thermogravimetric analysis coupled with differential scanning calorimetry (TGA-DSC). A-Ce 2 Si 2 O 7 was found to be stable in N 2 and air up to ~1483 K with anisotropic thermal expansion along the a and c axes (α a = 12.3 × 10 -6 K -1 and α c = 12.4 × 10 -6 K -1 ). Ce 4.67 (SiO 4 ) 3 O had a slow partial oxidation between 533 K and 873 K to a new nonstoichiometric phase Ce 3+ 1.67- xCe4 + x Ce 3+ 3 (SiO 4 ) 3 O 1+0.5x , followed by a thermal decomposition to CeO 2 and SiO 2 at ~1000 K in air. By using high temperature oxide melt solution calorimetry at 973 K with lead borate as the solvent, the standard enthalpy of formation was determined for A-Ce 2 Si 2 O 7 (-3825.1 ± 6.0 kJ/mol) and Ce 4.67 (SiO 4 ) 3 O (-7391.3 ± 9.5 kJ/mol). Finally, these thermodynamic parameters were compared with those of CeO 2 , CeSiO 4 , and other silicate oxyapatites for examining their chemical stability in high temperature environments relevant for aeronautical applications, mineral formation, and nuclear fuel cycle.

36 MATERIALS SCIENCE↗

Plutonium Co-precipitation with Calcite

The mobility of plutonium (Pu) in the environment is affected by Pu–mineral interactions, such as adsorption–desorption and structural incorporation. Calcite (CaCO 3 ) is a common secondary phase in near surface environments and a major component of many rocks and soils and is expected to form as an alteration product of cement-based materials planned for use in geological repositories. The reactivity of the calcite surface and its ability to tolerate significant variations in its chemical composition through substitution of Ca for other cations make calcite a potentially important sink for environmental contaminants. Here, single crystals of calcite were synthesized from aqueous solutions in equilibrium with air containing Pu as either Pu(VI) or Pu(IV) and characterized using a combination of laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) and X-ray absorption spectroscopy (XAS). These data are used to assess the amount, structure, and oxidation state of Pu co-precipitated into calcite, providing insight into the potential for Pu sequestration in calcite precipitates. Overall, the XAS and LA–ICP–MS data support the co-precipitation of plutonyl [Pu(VI/V)] in the bulk calcite, although the exact nature of the co-precipitated Pu complex is difficult to elucidate in the synthesized material. Co-precipitated plutonyl could be incorporated in either distorted Ca lattice sites or defect sites, and we provide evidence to suggest that Pu(VI) is reduced mainly to Pu(V) in the precipitated solid. LA–ICP–MS additionally shows that the co-precipitation of Pu(VI/V) is favored over the co-precipitation of Pu(IV). Altogether, our results suggest that Pu sequestration in calcite under environmental conditions could immobilize Pu and isolate it from groundwater interactions in contaminated environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling the Ionic Strength Effect on Diffusion in Clay. The DR-A Experiment at Mont Terri

Solute diffusion in compacted clays depends on ionic strength through its control on the thickness of the electrical double layer (EDL) on the charged clay surfaces. In the DR-A field experiment (Mont Terri, Switzerland), synthetic porewater was circulated through a borehole for 189 days, leading to the out-diffusion of a variety of tracers into the Opalinus Clay. The borehole solution was then replaced with a higher-salinity solution for an additional 540 days, leading to the diffusion of Cs + , Ca 2+ , Mg 2+ , and Sr 2+ back into the borehole and to an increase in the out-diffusion of anions (I - , Br - ) and 3 H. The experimental results were interpreted using the CrunchClay code, which includes a mean electrostatic potential model for the EDL. The EDL corresponds to a second continuum in addition to bulk electrically neutral porewater. Species-specific diffusion (Nernst-Planck equation) occurs through both domains. A 1D radial model considered a single pore diffusion coefficient (Dp = 10-9 m2/s) for cations and 3H in the bulk porosity, and a smaller D p (3 × 10 -10 m 2 /s) for anions. Dp values in the EDL were smaller (10 -11 m 2 /s), except for Cs + and K + (5 × 10 -10 and 2 × 10 -10 m 2 /s, respectively). The model reproduced well the experimental results and showed the capability to consider temporal changes in geochemical conditions affecting the transport and retention of potentially important radionuclide contaminants (e.g., 137 Cs + , 90 Sr 2+ , 129 I - ) in underground geological nuclear waste repositories. Finally, coupled multicomponent diffusion together with the electrostatic properties of the charged surfaces are essential in the development of predictive models for ion transport in clays.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Switchable Charge Storage Mechanism via in Situ Activation of MXene Enables High Capacitance and Stability in Aqueous Electrolytes

The need for reliable renewable energy storage devices has become increasingly important. However, the performance of current electrochemical energy storage devices is limited by either low energy or power densities and short lifespans. Herein, we report the synthesis and characterization of multilayer Ti 4 N 3 T x MXene in various aqueous electrolytes. We demonstrate that Ti 4 N 3 T x can be electrochemically activated through continuous cation intercalation over a 10 day period using cyclic voltammetry. A wide operating window of 2 V is maintained throughout activation. After activation, capacitance at 2 mV s -1 increases by 300%, 140%, and 500% in 1 M H2SO4, 1 M MgSO4, and 1 M KOH, respectively, while maintaining ~600 F g -1 at 2 mV s–1 after 50000 cycles in 1 M H 2 SO 4 . This activation process is possibly attributed to the unique morphology of the multilayered material, allowing cation intercalation to increase access to redox-active sites between layers. This work adds to the growing repository of electrochemically stable MXenes reported for aqueous energy storage applications. These findings offer a reliable option for reliable energy storage devices with potential applications in large-scale grid storage and electric vehicles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Glass-Bonded Monazite Waste Forms for Lanthanide and Actinide Immobilization: From Theoretical Design to Scale-Up Production and Characterization

The development of nuclear waste forms for both existing and future nuclear wastes is critical to ensuring global environmental safety. This study focuses on waste management from molten salt reactors, where fuel exists in a salt form and could be processed in real time for the removal of neutron poisons such as xenon isotopes (e.g., 135 Xe) and rare earth elements (REEs, e.g., 149 Sm). To ensure safe, stable, and long-term disposal in geological repositories, REEs must be incorporated into a durable waste form. Iron-phosphate glasses are a promising candidate due to their low melting points, high chemical durability, and their ability to incorporate high concentrations of REEs. In this study, we successfully prepared iron-phosphate glass waste forms with high Nd loadings (up to 37 mass %) in batch sizes ranging from small (23 g) to large (1600 g). The resulting materials contained up to 75 mass % NdPO 4 , contributing to their mechanical resilience and exceptional chemical durability. These findings highlight the potential of iron-phosphate glasses as high-efficiency, chemically durable waste forms and demonstrate the successful transition from theoretical design to scaled-up production.

amorphous materials↗

Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

Abstract DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

Plahar, Hector [DOE Agile BioFoundry , , ,; DOE Jo↗

Immobilization of 99-Technetium (VII) by Fe(II)-Goethite and Limited Reoxidation

During the nuclear waste vitrification process volatilized {sup 99}Tc will be trapped by melter off-gas scrubbers and then washed out into caustic solutions, and plans are currently being contemplated for the disposal of such secondary waste. Solutions containing pertechnetate [{sup 99}Tc(VII)O{sub 4}{sup -}] were mixed with precipitating goethite and dissolved Fe(II) to determine if an iron (oxy)hydroxide-based waste form can reduce Tc(VII) and isolate Tc(IV) from oxygen. The results of these experiments demonstrate that Fe(II) with goethite efficiently catalyzes the reduction of technetium in deionized water and complex solutions that mimic the chemical composition of caustic waste scrubber media. Identification of the phases, goethite + magnetite, was performed using XRD, SEM and TEM methods. Analyses of the Tc-bearing solid products by XAFS indicate that all of the Tc(VII) was reduced to Tc(IV) and that the latter is incorporated into goethite or magnetite as octahedral Tc(IV). Batch dissolution experiments, conducted under ambient oxidizing conditions for more than 180 days, demonstrated a very limited release of Tc to solution (2-7 {micro}g Tc/g solid). Incorporation of Tc(IV) into the goethite lattice thus provides significant advantages for limiting reoxidation and curtailing release of Tc disposed in nuclear waste repositories.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NCAR Release of CAM‐SE in CESM2.0: A Reformulation of the Spectral Element Dynamical Core in Dry‐Mass Vertical Coordinates With Comprehensive Treatment of Condensates and Energy

Abstract It is the purpose of this paper to provide a comprehensive documentation of the new NCAR (National Center for Atmospheric Research) version of the spectral element (SE) dynamical core as part of the Community Earth System Model (CESM2.0) release. This version differs from previous releases of the SE dynamical core in several ways. Most notably the hybrid sigma vertical coordinate is based on dry air mass, the condensates are dynamically active in the thermodynamic and momentum equations (also referred to as condensate loading), and the continuous equations of motion conserve a more comprehensive total energy that includes condensates. Not related to the vertical coordinate change, the hyperviscosity operators and the vertical remapping algorithms have been modified. The code base has been significantly reduced, sped up, and cleaned up as part of integrating SE as a dynamical core in the CAM (Community Atmosphere Model) repository rather than importing the SE dynamical core from High‐Order Methods Modeling environment as an external code.

54 ENVIRONMENTAL SCIENCES↗

Predicting Effective Diffusion Coefficients in Mudrocks Using a Fractal Model and Small-Angle Neutron Scattering Measurements

The determination of effective diffusion coefficients of gases or solutes in the water–saturated pore space of mudrocks is time consuming and technically challenging. Yet, reliable values of effective diffusion coefficients are important to predict migration of hydrocarbon gases in unconventional reservoirs, dissipation of (explosive) gases through clay barriers in radioactive waste repositories, mineral alteration of seals to geological CO 2 storage reservoirs and contaminant migration through aquitards. In this study, small angle and very small angle neutron scattering techniques have been utilized to determine a range of transport properties in mudrocks, including porosity, pore size distributions and surface and volume fractal dimensions of pores and grains, from which diffusive transport parameters can be estimated. Using a fractal model derived from Archie's Law, we calculate effective diffusion coefficients from these parameters and compare them to laboratory–derived effective diffusion coefficients for CO 2 , H 2 , CH 4 and HTO on either the same or related mudrock samples. The samples include Opalinus Shale from the underground laboratory in Mont Terri, Switzerland; Boom Clay from a core drilled in Mol, Belgium and a marine claystone cored in Utah, USA. The predicted values were compared to laboratory diffusion measurements. The measured and modeled diffusion coefficients show good agreement, differing generally by less than factor 5. Furthermore, neutron or X–ray scattering analysis is therefore proposed as a novel method for fast, accurate estimation of effective diffusion coefficients in mudrocks, together with simultaneous measurement of multiple transport parameters including porosity, pore size distributions and surface areas, important for (reactive) transport modelling.

58 GEOSCIENCES↗

Evolution of the Percolation Threshold in Muds and Mudrocks During Burial

Abstract Muds and mudrocks are important barriers to flow and perform this role over their entire depositional history, from mediating sediment‐ocean methane exchange to preventing leakage from hydrocarbon reservoirs, CO 2 sequestration targets, or nuclear waste repositories. It is well established that the percolation threshold, which is the fluid saturation at which percolation occurs, is directly related to the pressure sealing capacity of a mud or mudrock. However, the evolution of the percolation threshold during burial and diagenesis is not well understood. Using a data set of natural muds and mudrocks and resedimented laboratory mixtures, we show that the percolation threshold is strongly controlled by porosity, achieving a minimum of 0.10–0.30 at a porosity of 0.40, and increasing as porosity increases or decreases from that value, to as high as 0.60 at deposition and >0.80 at porosity <0.10. This implies a highly disconnected pore network at high and low porosities.

Daigle, Hugh↗

A Guide to Using GitHub for Developing and Versioning Data Standards and Reporting Formats

Abstract Data standardization combined with descriptive metadata facilitate data reuse, which is the ultimate goal of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Community data or metadata standards are increasingly created through an approach that emphasizes collaboration between various stakeholders. Such an approach requires platforms for collaboration on the development process that centers on sharing information and receiving feedback. Our objective in this study was to conduct a systematic review to identify data standards and reporting formats that use version control for developing data standards and to summarize common practices, particularly in earth and environmental sciences. Out of 108 data standards and reporting formats identified in our review, 32 used GitHub as the version control platform, and no other platforms were used. We found no universally accepted methodology for developing and publishing data standards. Many GitHub repositories did not use key features that could help developers to gather user feedback, or to create and revise standards that build on previous work. We provide guidance for community‐driven standard development and associated documentation on GitHub based on a systematic review of existing practices.

54 ENVIRONMENTAL SCIENCES↗

A Comprehensive Northern Hemisphere Particle Microphysics Data Set From the Precipitation Imaging Package

Microphysical observations of precipitating particles are critical data sources for numerical weather prediction models and remote sensing retrieval algorithms. However, obtaining coherent data sets of particle microphysics is challenging as they are often unindexed, distributed across disparate institutions, and have not undergone a uniform quality control process. This work introduces a unified, comprehensive Northern Hemisphere particle microphysical data set from the National Aeronautics and Space Administration precipitation imaging package (PIP), accessible in a standardized data format and stored in a centralized, public repository. Data is collected from 10 measurement sites spanning 34° latitude (37°N–71°N) over 10 years (2014–2023), which comprise a set of 1,070,000 precipitating minutes. The provided data set includes measurements of a suite of microphysical attributes for both rain and snow, including distributions of particle size, vertical velocity, and effective density, along with higher-order products including an approximation of volume-weighted equivalent particle densities, liquid equivalent snowfall, and rainfall rate estimates. The data underwent a rigorous standardization and quality assurance process to filter out erroneous observations to produce a self-describing, scalable, and achievable data set. Case study analyses demonstrate the capabilities of the data set in identifying physical processes like precipitation phase-changes at high temporal resolution. Bulk precipitation characteristics from a multi-site intercomparison also highlight distinct microphysical properties unique to each location. This curated PIP data set is a robust database of high-quality particle microphysical observations for constraining future precipitation retrieval algorithms, and offers new insights toward better understanding regional and seasonal differences in bulk precipitation characteristics.

54 ENVIRONMENTAL SCIENCES↗

Spent Nuclear Fuel Disposition

One interdisciplinary field devoted to achieving the end-state of used nuclear fuel (UNF) through reuse and/or permanent disposal. The reuse option aims to make use of the remaining energy content in UNF and reduce the amount of long-lived radioactive materials that require permanent disposal. The planned approach in the U.S., as well as in many other countries worldwide, is direct permanent disposal in a deep geologic repository. Used nuclear fuel is fuel that has been irradiated in a nuclear reactor to the point where it is no longer capable of sustaining operational objectives. The vast majority (by mass) of UNF is from electricity generation in commercial nuclear power reactors. Furthermore, the other main source of UNF in the U.S. is the Department of Energy’s (DOE) and other federal agencies’ operation of reactors in support of federal government missions, such as materials production, nuclear propulsion, research, testing, and training. Upon discharge from a reactor, UNF emits considerable heat from radioactive decay. Some period of active on-site cooling (e.g., 2 or more years) is typically required to facilitate efficient packaging and transportation to a disposition facility. Hence, the field of UNF disposition broadly includes storage, transportation and ultimate disposition. See also: Nuclear Fission (content/nuclear-fission/458400), Nuclear Fuels (/content/nuclear-fuels/458600), Nuclear Fuel Cycle (/content/nuclear-fuel-cycle/458500), Nuclear Fuels Reprocessing (/content/nuclear-fuels-reprocessing/458700), Nuclear Power (/content/nuclear-power/459600), Nuclear Reactor (/content/nuclear-reactor/460100), Radiation (/content/radiation/566300), and Radioactive Waste Management (/content/radioactive-waste-management/568900).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

59 BASIC BIOLOGICAL SCIENCES↗